GenomesPublic server (cyano2)
- Django: Update Django to the latest SVN v1.1. Development server is already updated.Database updates
- GenBank Update: Working with EBI to update MED4- Waiting on GenBank Update MIT9313
- (Add new genes and alternative locus tags). Once these get into the system, update their gb_tags in data_protein table.
- Microarray: newly analyzed data using the latest annotation cdf file
- Database: Flag "core" or "flexible" protein clusters.
Data Import to ProPortal
- Chisholm lab publications- the 3 published phage genomes
- Annotate 9202 and add this genome to ProPortal
- Reannotate the gene clusters
- Ecotype data
- phage-infection microarray data
- operon predictions
- pfam/tigrfam domain assignments
- link publications to individual genes
Data analysis
- Assign GOS clusters to individual proteins and protein clusters- Map GOS peptides, transcripts, reads to genes
- Build PHYML trees for all protein clusters plus closely related clusters. - A few more marine Synechococcus genomes have been available. Go through our genome annotation pipeline? - P9202 annotations. Waiting for MicrobesOnline to finish BLAST, HMM and Tree computations. We'll be assigning gene name, description, E.C. numbers and reclustering protein genes (core vs flexible) - Build MSA/HMM profiles of protein clusters, thus we do not have to "recluster" protein genes every time there's a new genome sequenced.
Data download
- Genome seqs, annotations- Microarray data, cel files, cdf, master_gene_table
Other publications
Data visualization
- Genome page: COG function pie charts- Genome page: Core vs flexible charts
- Genome page: Links to genes
- Genome page/Protein page: Develop a simple genome browser? Main track will be genes of a selected genome. Optional tracks are: operon, protein cluster flag (core, HL-specific, LL-specific, flexible, orphan), COG function code (colored), KEGG pathway color-coded, GOS read abundance/gene length.
- Protein cluster page: A newick tree viewer, which allows users to reroot the tree.
Site Navigation
- Help page- Site map
- Site search (different from the database search). Or a combination of the two.
Site Appearance
- Site logo: Prochlorococcus Portal- italicize Prochlorococcus